Denaturing high-performance liquid chromatography (DHPLC)-based DNA fragment analysis is a high-throughput technology that can be used to obtain information on both genetic alterations and gene expression. By using different approaches based on polymerase chain reaction, this technique can be used to determine loss or gain of an allele, to quantitate the amount of RNA expressed, and to detect a single nucleotide change. Applications of DHPLC to molecular carcinogenesis include genotyping of transgenic animals; determination of allelic imbalances, including loss of heterozygosity in tumors; measurement of changes in gene expression; and detection of DNA polymorphisms and point mutations. In our laboratories DHPLC has been validated and used to genotype an Eker rat colony, to study the genetic profile of renal cell carcinomas, to quantitate expression of the keratinocyte lipid-binding protein gene in 8-lipoxygenase transgenic mice, and to detect polymorphisms and a point mutation in the tuberous sclerosis 2 tumor suppressor gene in t-haplotype mice.